Fossilization is an exceptionally rare occurrence, because most components of formerly-living things tend to decompose relatively quickly following death. In order for an organism to be fossilized, the remains normally need to be covered by sediment as soon as possible. However there are exceptions to this, such as if an organism becomes frozen, desiccated, or comes to rest in an anoxic (oxygen-free) environment. There are several different types of fossils and fossilization processes.

Due to the combined effect of taphonomy and simple mathematical chance, fossilization tends to favor organisms with hard body parts, those that were widespread, and those that lived for a long time. On the other hand, it is very unusual to find fossils of small, soft bodied, geographically restricted and geologically ephemeral organisms, because of their relative rarity and low likelihood of preservation.

Larger specimens (macrofossils) are more often observed, dug up and displayed, although microscopic remains (microfossils) are actually far more common in the fossil record.

Some casual observers have been perplexed by the rarity of transitional species within the fossil record. The conventional explanation for this rarity was given by Charles Darwin, who stated that "the extreme imperfection of the geological record," combined with the short duration and narrow geographical range of transitional species, made it unlikely that many such fossils would be found. Simply put, the conditions under which fossilization takes place are quite rare; and it is highly unlikely that any given organism will leave behind a fossil. Eldredge and Gould developed their theory of punctuated equilibrium in part to explain the pattern of stasis and sudden appearance in the fossil record. Furthermore, in the strictest sense, nearly all fossils are "transitional," due to the improbability that any given fossil represents the absolute termination of an evolutionary path.

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